Methods for diagnosing tuberous sclerosis by detecting mutation in the TSC-1 gene

ABSTRACT

The present invention is directed to a tumor suppressor protein which has been designated hamartin and to the gene, TSC1, which encodes this protein. Mutations in the gene have been found to be associated with certain types of tuberous sclerosis and this has served as a basis for a diagnostic method designed to identify patients that have, or are likely to develop, symptoms associated with this disease. The introduction of the TSC1 gene and subsequent expression of hamartin into cells may be used as a means for treating tuberous sclerosis and other conditions characterized by abnormal cellular growth.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a division of U.S. application Ser. No. 09/457,708, now U.S. Pat. No. 6,326,483 filed Dec. 10, 1999, which is a continuation of international application no. PCT/US98/14567, having an international filing date of Jul. 15, 1998 (now abandoned), which claims the benefit of provisional application no. 60/053,107, filed Jul. 18, 1997 (now abandoned).

STATEMENT OF GOVERNMENT SUPPORT

The work leading to this invention was supported by one or more grants from the U.S. Government. The U.S. Government therefore has certain rights in the invention.

FIELD OF THE INVENTION

The present invention is directed to the gene TSC1 and to the protein it encodes. TSC1 has the characteristics of a tumor suppressor gene and is often mutated in individuals with a familial form of tuberous sclerosis. The invention also encompasses methods that relate to the gene and gene product.

BACKGROUND OF THE INVENTION

Tuberous sclerosis (TSC) is an autosomal dominant disorder characterized by the development of unusual tumor-like growths (hamartomas) in a variety of organ systems (Gomez, M. R., Ann. N.Y. Acad. Sci. 615:1-7 (1991); Kwiatkowski, et al., Arch. Dermatol. 130:348-354 (1994)). The development of cortical tubers in the brain (regions of abnormal cortical architecture with distinctive large neuronal cells) causes some of the most problematic clinical manifestations of TSC: mental retardation, epilepsy and abnormal behavioral phenotypes including autism and attention deficit-hyperactive disorder (Hunt, et a., J. Autism. Dev. Disorder 23:323-339 (1993); Smalley, et al., J. Autism. Dev. Disorder 22:339-355 (1992)). Other organ systems commonly involved in TSC include the skin, heart, and kidneys (Kwiatkowski, et al., Arch. Dermatol. 130:348-354 (1994)). The lesions seen are often pathognomonic of TSC and include facial angiofibromas, subungual fibromas, forehead plaque, Shagreen patches, cardiac rhabdomyomas and renal angiomyolipomas and cysts. Renal cell carcinoma also occurs at higher frequency and at an earlier age of onset in TSC patients than in normal individuals (Bjornsson, et al., Am. J. Path. 149:1201-1208 (1996); Cook, et al., J. Med. Genet. 33:480-484 (1996)). About one-third of TSC cases are familial with the remainder being sporadic, i.e., occurring in the absence of a family history of the disease.

Linkage of TSC to 9q34 was first reported in 1987 and this locus was denoted TSC1 (Fryer, et al., Lancet i:659-661 (1987)). Subsequent studies provided strong evidence for locus heterogeneity and led to the identification of 16p13 (denoted the TSC2 locus) as a second genomic region showing linkage in some TSC families (Kandt, et al., Exp. Neurol. 104:223-228 (1989)). Among families large enough to permit linkage analysis, approximately half show linkage to 9q34 and half to 16p13 (Janssen, et al., Hum. Genet. 94:437-440 (1994)).

The TSC2 gene has been isolated and found to consist of 41 coding exons distributed over 45 kb of genomic DNA. It has a message length of 6 kb and encodes several alternatively spliced transcripts and predicted proteins of 1784-1807 amino acids (Maheshwar, et al., Hum. Mol. Genet. 5:131-137 (1996); Xu, et al., Genomics 27:475-480 (1995)). The occurrence of inactivating germline mutations in TSC2 in patients with tuberous sclerosis and loss of heterozygosity (LOH) at the TSC2 locus in up to 50% of TSC-associated hamartomas support a tumor suppressor function for TSC2 (Carbonara, et al., Cancer 15:18-25 (1996); Sepp, et al., J. Med. Genet. 33:962-964 (1996)).

Although the TSC2 gene has been isolated and characterized, identification of the TSC1 gene on 9q34 has proven difficult for a number of reasons. Conflicting positional information has been generated by the analysis of meiotic recombination events in TSC families; large genomic rearrangements (e.g., translocations involving this region) have not been discovered; and several parts of the region are unstable in multiple cloning vectors. In addition, the region contains a number of different genes, any one of which could potentially be TSC1. The unambiguous identification of the TSC1 gene would represent a significant advance in several different respects. First, assays designed to identify mutations in TSC1 could be used to help diagnose this condition in patients exhibiting clinical manifestations suggesting that they may suffer from tuberous sclerosis. Similarly, such assays could be used to help identify patients likely to develop the disorder or likely to pass it on to their offspring.

Therapeutically, the identification of the TSC1 gene and its product may provide a tool for the treatment of abnormal cellular growth. In the case of tuberous sclerosis patients, the introduction and expression of the normal TSC1 gene in place of mutated counterparts should help to prevent the development of hemartomas associated with the disease. In addition, the ability to inhibit uncontrolled cellular growth suggests that TSC1 and its product may have therapeutic applications for other conditions characterized by neoplastic growth.

SUMMARY OF THE INVENTION

The present invention is based upon the discovery of a gene (TSC1) which is found within the 9q34 region of chromosome 9. Mutations in TSC1 are associated with familial forms of tuberous sclerosis and the encoded protein, hamartin, has the characteristics of a tumor suppressor.

In its first aspect, the invention is directed to a protein, except as existing in nature, having an amino acid sequence consisting essentially of the sequence shown in FIG. 4 (SEQ ID NO:2). The term “consisting essentially of,” is meant to encompass proteins having exactly the same amino acid sequence as shown in the figure, as well as proteins with differences that are not substantial as evidenced by their retaining the basic, qualitative functional properties of hamartin. The phrase “except as existing in nature” encompasses substantially purified forms of the protein as well as forms made by recombinant or synthetic means. A “substantially purified” protein is one that has been separated from other accompanying biological components and will typically comprise at least 85% of a sample, with greater percentages being preferred. Many means are available for assessing the purity of a protein within a sample including analysis by polyacrylamide gel electrophoresis, chromatography and analytical centrifugation.

The invention also encompasses antibodies that bind specifically to hamartin (i.e., that have at least a 100-fold greater affinity for hamartin than any other undenatured protein), and antibodies made by a process involving the injection of a pharmaceutically acceptable preparation of hamartin into an animal capable of antibody production. In a preferred embodiment, monoclonal antibody to hamartin is produced by injecting the pharmaceutically acceptable preparation into a mouse and then fusing mouse spleen cells with myeloma cells.

The invention is also directed to a polynucleotide, except as existing in nature, which encodes a protein consisting essentially of the amino acid sequence of FIG. 4 (SEQ ID NO:2), expression vectors comprising such polynucleotides, and host cells transformed with such vectors. Also included is the human hamartin protein produced by host cells made in this manner. Preferably, the polynucleotide encoding the human hamartin has the sequence shown in FIG. 4 (i.e., that it comprises nucleotides 222-3713 of SEQ ID NO:1). It is also preferred that the vectors and host cells prepared for the expression of hamartin use this particular polynucleotide.

In another aspect, the present invention is directed to a method for identifying a patient that has, or is likely to develop, tuberous sclerosis by determining if the TSC1 gene of the patient is mutated, i.e., by determining whether it contains nucleotide additions, substitutions, or deletions relative to the wild-type TSC1 sequence. The patients examined by this method will typically be those that are exhibiting clinical characteristics suggesting that they may have tuberous sclerosis or individuals that have family members diagnosed as having the disease. In the first case, the method will be used in order to make or confirm a diagnosis and, in the latter case, it will be used to predict whether the patient or their offspring are likely to develop the disease. In general, the likelihood of a patient having or developing tuberous sclerosis increases in proportion to the number and seriousness of TSC1 mutations. Serious mutations include those that cause a frameshift resulting in the misreading of subsequent amino acids or that correspond to specific mutations that have been associated with tuberous sclerosis (see e.g., Table 4).

Any means may be used for determining the extent to which the TSC1 gene has been mutated, including direct nucleotide sequence analysis or hybridization under conditions selected to reveal mutations. However, the preferred method is to amplify one or more regions of the TSC1 gene using the polymerase chain reaction (PCR) and to then analyze the amplification products, e.g., by sequence analysis, heteroduplex analysis, or single strand conformation polymorphism analysis. In a preferred embodiment, the region amplified corresponds to one or more of exons 3-23, with the most preferred exons being 7, 9, 10, 15, 17, 18, 19 and 20.

An analysis of the characteristics of the hamartin protein indicates that it falls within the class of proteins that have been termed “tumor suppressors.” Mutations in these proteins which lead to a loss of function are oncogenic and it is recognized that the wild-type forms of the proteins suppress abnormal cellular proliferation. Examples of genes that have been found to encode tumor suppressors include the retinoblastoma susceptibility gene, the p53 gene, and the neurofibromatosis type 1 gene (Weinberg, R. A., Science 254:1138-1146 (1991)). Thus, the present invention is directed to a method for treating or preventing the abnormal proliferation of mammalian cells by introducing into the cells DNA encoding hamartin. The DNA must be incorporated into the cells in such a manner that it will undergo expression. In general, this means that the gene must be either operably linked to a promoter that is introduced at the same time as the gene itself or homologous recombination must be used to position the gene downstream from an endogenous promoter. This method may be carried out either on cells in vitro or in vivo. In either case, it is preferred that the cells be selected because they have a mutated form of the TSC-1 gene characteristic of tuberous sclerosis. The most preferred cells for use in conjunction with the method are those containing mutations in exons 3-23, and especially those with mutations in one or more of 7, 9, 10, 15, 17, 18, 19 and 20.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: The TSC1 Region on Chromosome 9: The ideogram (top) represents a normal G-banded metaphase chromosome 9, with the TSC1 region located at 9q34. The male genetic map (middle) shows selected anchor polymorphic loci mapped to 9q34 and the TSC1 candidate region extending from D9S149 to D9S114. The detailed physical map of the candidate region (bottom) shows the positions of polymorphic markers and key recombination events in affected members (filled arrows) and unaffected members (open arrows) of families showing linkage of TSC to 9q34; the approximate positions of MluI sites, M, (with sites which partially cut genomic DNA shown in brackets) and probes used to screen the region for rearrangement in patients with TSC using pulsed field gel electrophoresis; genes previously mapped to the TSC1 candidate region; novel cDNAs isolated from the region; ESTs mapped to the region during this study; and putative genes predicted by GRAIL analysis of genomic sequence. Distances (in kb) from the proximal flanking marker D9S2127 were derived from the sizes of EcoRI fragments in a cosmid contig which spanned the region with one gap of 20 kb near D9S1793.

FIG. 2 (panels A-D): Identification of Mutations in TSC1 Exon 15: Panel A shows a heteroduplex analysis performed on positive samples from the screening population. Panel B shows the results of a sequence analysis that reflects a 2105 del AAAG mutation. The sequence reactions were done in antisense orientation, so that reading from the top down b2083-2124 of the normal sequence is shown. The allele sequenced on the left has the deletion, the middle allele is normal, and the sequence on the right is the heteroduplex product with both alleles. Panel C shows the results of an analysis performed in a patient with sporadic TSC. It can be seen that the heteroduplex mobility shift is not present in either parent. Panel D shows the segregation of heteroduplex mobility shifts in a large family with TSC and the digestion of amplification products with MwoI in another family. The results suggest segregation of the 2105delAAAG mutation with the disease.

FIG. 3: Northern Blot Analysis of TSC1 Expression: Each lane shown in the figure contains 2 micrograms of poly A+RNA from adult human organs. The probe used consisted of nucleotides 1100-2200 of the TSC1 gene. The lane labeled “muscle” is skeletal muscle.

FIGS. 4(a)-4(c): Sequence and Predicted Amino Acid Sequence of the TSC1 Gene. A portion of the nucleotide sequence determined for the TSC 1 gene is shown in the figure. The complete sequence, including a 3′ untranslated region of approximately 4.5 kb, is shown as SEQ ID NO:1. Nucleotides 222-3713 encode the hamartin structural sequence. The figure also shows the predicted amino acid sequence of hamartin. This has been designated as SEQ ID NO:2. Amino acids 127-144 correspond to a potential transmembrane domain and amino acids 730-965 correspond to a coiled coil domain.

FIG. 5: Genomic Structure of TSC 1: The genomic structure of the TSC1 gene, including the positions of the 23 exons, is shown in the figure.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is directed to the hamartin protein, genetic sequences encoding the protein, a method for identifying patients that have or are likely to develop tuberous sclerosis and a method for treating or preventing the abnormal proliferation of mammalian cells. The hamartin protein and the nucleic acids encoding the protein are defined by their structures as shown in FIG. 4.

It will be understood that the present invention encompasses not only sequences identical to those shown in the figures, but also sequences that are essentially the same as evidenced by the protein retaining its basic functional characteristics. For example, it is well known that techniques such as site-directed mutagenesis may be used to introduce variations in a protein's structure. Variations in hamartin introduced by this or by a similar method are encompassed by the invention provided that the resulting protein retains its biological properties, particularly the ability to suppress abnormal cellular growth.

I. Nucleic Acid Sequences Coding for Hamartin

DNA sequences coding for hamartin may be obtained from any tissue or cellular source which expresses the gene. The cells used may either be cultured cells that have not undergone transformation or cell lines specifically engineered to express recombinant hamartin. Many methods are available for isolating DNA sequences and may be adapted for the isolation of hamartin nucleic acid (see, e.g., Sambrook, et al., Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Press (1989)). One preferred method is to screen a cDNA library that has been prepared by reverse transcribing mRNA isolated from tissues or cells known to express the gene. The library may be prepared from, for example, human fetal brain tissue.

It is expected that a wide variety of probes specific for hamartin can be used equally well for the screening of cDNA libraries. One way to easily produce a large amount of probe is to use the polymerase change reaction (PCR) to amplify the desired sequence from a cDNA library. A listing of primers that have been found to be suitable for amplifying specific exons of the hamartin gene is shown in Table 3.

Amplified fragments can be size fractionated on an agarose gel and the selected fragments (based upon the expected size of the exon amplified) inserted into an appropriate vector and introduced into competent cells by any of the established methods for cell transformation, e.g. by calcium phosphate precipitation. Transformed cells containing the DNA of interest may be identified either by hybridization with a radiolabeled probe specific for the exon in question or by PCR amplification using primers complementary to a region of the exon. The DNA inserts present in the cells are excised, purified and labeled with ³²P. The labeled DNA fragments thus produced are used as probes for screening a cDNA library for hamartin. The presence of the correct sequence in selected cells may be confirmed by DNA sequencing and, if necessary, partial clones may be spliced together to form a full length sequence.

Although the above procedure is suitable for obtaining hamartin nucleic acid, it is expected that alternative techniques can be developed with relatively little effort. Thus, cDNA libraries may be screened using probes synthesized based upon the sequence shown in FIG. 4. In general, the probes should be at least 14 nucleotides long and should not be selected from a region known to be conserved among proteins. Alternatively, using the sequences shown in the figure, it should be possible to select PCR primers and amplify the full length hamartin sequence.

II. Production and Isolation of Hamartin Recombinant Protein

In order to express recombinant hamartin, the DNA encoding the structural sequence of the protein must be placed in a vector containing transcriptional and translational signals recognizable by an appropriate host. The cloned hamartin sequences, preferably in double stranded form, are inserted into the expression vector in an operable linkage, i.e., they are positioned so as to be under the control of regulatory sequences found in the vector and in such a manner that mRNA is produced which is translated into the hamartin amino acid sequence.

Expression of the hamartin protein in different hosts may result in different post-translational modifications that can, potentially, alter the properties of the protein. Preferably, nucleic acid encoding hamartin is expressed in eukaryotic cells, especially mammalian cells. These cells provide post-translational modifications which, inter alia, aid in the correct folding of the protein. Mammalian cells that may be used include, without limitation, NIH-3T3 cells, CHO cells, HeLA cells, LM(tk-) cells, etc. Vectors suitable for each of these various cell types are well known in the art (see e.g. Sambrook, et al., supra). Preferred eukaryotic promoters include that of the mouse metallothionein I gene, the TK promoter of Herpes virus; the SV40 early promoter; and the CMV early promoter. Some examples of suitable prokaryotic promoters include those capable of recognizing T4 polymerases, the P_(R) and P_(L) promoters of bacteriophage lambda, and the trp, recA, heat shock and lacZ promoters of E. coli.

Expression vectors may be introduced into host cells by methods such as calcium phosphate precipitation, microinjection, electroporation or viral transfer. Cells expressing hamartin can be selected using methods well known in the art. One simple method for confirming the presence of the hamartin nucleic acid in cells is to perform PCR amplification using the procedures and primers discussed above.

Recombinant hamartin protein may be purified using standard techniques well known in the art. These may include filtration, precipitation, chromatography and electrophoretic methods. Purity can be assessed by performing electrophoresis on a polyacrylamide gel and visualizing proteins using standard staining techniques.

III. Antibodies to Hamartin

The present invention is also directed to antibodies that bind specifically to hamartin and to a process for producing such antibodies. Antibodies that “bind specifically to hamartin” are defined as those that have at least a 100 fold greater affinity for hamartin than for any other undenatured protein. The process for producing such antibodies may involve either injecting the hamartin protein itself into an appropriate animal or, preferably, injecting short peptides made to correspond to different regions of hamartin. The peptides should be at least 5 amino acids in length and should be selected from regions believed to be unique to the protein. Thus, highly conserved regions should generally be avoided in selecting peptides for the generation of antibodies. Methods for making and detecting antibodies are well known to those of skill in the art as evidenced by standard reference works such as: Harlow, et al., Antibodies, A Laboratory Manual, Cold Spring Harvar Laboratory, M.Y. (1988); Klein, Immunology: The Science of Self-Nonself Discrimination (1982); Kennett, et al., Monoclonal Antibodies and Hybridomas: A New Dimension in Biological Analyses (1980); and Campbell, “Monoclonal Antibody Technology,” in Laboratory Techniques in Biochemistry and Molecular Biology (1984).

“Antibody,” as used herein, is meant to include intact molecules as well as fragments which retain their ability to bind to antigen (e.g., Fab and F(ab′)₂ fragments). These fragments are typically produced by proteolytically cleaving intact antibodies using enzymes such as papain (to produce Fab fragments) or pepsin (to produce F(ab′)₂ fragments). The term “antibody” also refers to both monoclonal antibodies and polyclonal antibodies. Polyclonal antibodies are derived from the sera of animals immunized with the antigen. Monoclonal antibodies can be prepared using hybridoma technology (Kohler, et al., Nature 256:495 (1975); Hammerling, et al., in: Monoclonal Antibodies and T-Cell Hybridomas, Elsevier, N.Y., pp. 563-681 (1981)). In general, this technology involves immunizing an animal, usually a mouse, with either intact hamartin or a fragment derived from hamartin. The splenocytes of the immunized animals are extracted and fused with suitable myeloma cells, e.g., SP₂O cells. After fusion, the resulting hybridoma cells are selectively maintained in HAT medium and then cloned by limiting dilution (Wands, et al., Gastroenterology 80:225-232 (1981)). The cells obtained through such selection are then assayed to identify clones which secrete antibodies capable of binding to hamartin.

The antibodies or fragments of antibodies of the present invention may be used to detect the presence of hamartin protein in any of a variety of amino assays. For example, antibodies may be used in radioimmunoassays or in immunometric assays, also known as “two-site” or “sandwich” assays (see Chard, T., “An Introduction to Radioimmune Assay and Related Techniques,” in: Laboratory Techniques in Biochemistry and Molecular Biology, North Holland Publishing Co., N.Y. (1978)). In a typical immunometric assay, a quantity of unlabeled antibody is bound to a solid support that is insoluble in the fluid being tested, e.g. blood, lymph, cellular extracts, etc. After the initial binding of antigen to immobilized antibody, a quantity of detectably labeled second antibody (which may or may not be the same as the first) is added to permit detection and/or quantitation of bound antigen (see e.g. Radioimmune Assay Method, Kirkham et al., ed., pp. 199-206, E&S Livingstone, Edinburgh (1970)). Many variations of these types of assays are known in the art and may be employed for the detection of hamartin.

Antibodies may also be developed that are specific for mutated exons of hamartin that have been shown to be associated with TSC. A list of specific mutations for exons 7, 9, 10, 15, 17, 18, 19 and 20 may be found in Table 4. One or more of these mutations may be introduced into the TSC1 DNA by a variety of techniques. The appropriate exon may then be amplified, cloned into an appropriate expression vector and recombinantly produced. Monoclonal antibodies may be generated by the techniques discussed above and those specific for mutated forms of hamartin selected by comparing their ability to bind to the mutated exon and its wild-type counterpart.

Antibodies to hamartin may also be used in the purification of either the intact protein or fragments of the protein (see generally, Dean et al., Affinity Chromatography, A Practical Approach, IRL Press (1986)). Typically, antibody is immobilized on a chromatographic matrix such as Sepharose 4B. The matrix is then packed into a column and the preparation containing hamartin is passed through under conditions that promote binding, e.g. under conditions of low salt. The column is then washed and bound hamartin is eluted using a buffer that promotes dissociation from antibody, e.g. buffer having an altered pH or salt concentration. The eluted hamartin may be transferred into a buffer of choice, e.g. by dialysis, and either stored or used directly.

IV. Assays for Patients that Have or are Likely to Develop Tuberous Sclerosis

Although there are clinical criteria for determining whether a patient has tuberous sclerosis, a diagnosis may be difficult to make in cases where symptoms are marginal or the onset of the disease is protracted. The present invention provides a diagnostic method for confirming that a patient has tuberous sclerosis and for identifying individuals that carry forms of the TSC1 gene that are likely to lead to the onset of the disease either in themselves or their offspring.

The basic concept that reduced or aberrant expression of the TSC1 gene is associated with tuberous sclerosis has been established by the experiments discussed below in the Examples section. This concept is the basis of the present diagnostic method which has as its essential feature the determination of whether mutations exist in the TSC1 nucleotide sequence or whether the gene is under-expressed. Table 4 lists a series of mutations that have been found to be specifically associated with patients having TSC. An indication that one or more of these mutations are present would be a strong indication that the patient examined, or their offspring, are likely to develop TSC-associated symptoms.

Other mutations would also be indicative of a propensity to the disease with the likelihood of disease development or presence correlating directly with the seriousness of the mutations in terms of disrupting the biological function of the gene product. For example, deletions, rearrangements or additions that resulted in a substantial misreading of the hamartin amino acid sequence would be a very strong positive result The same is true with regard to the expression of the gene. Thus, patients who expressed substantially less (e.g., 50% or less) of the hamartin protein relative to control individuals known not to have TSC or come from a family in which the disease is present, would stand a strong likelihood of developing TSC-associated symptoms even if they had a normal TSC1 genotype.

Methods for analyzing mutations within the TSC2 gene have been established (WO 95/18226; Vrtel, et al., J. Med. Genet. 33:47-51 (1996); Wilson et al., Hum. Mol. Genet. 5:249-256 (1996)) and, with minor modifications, these can be readily adapted to the analysis of mutations in TSC1. Thus, a preferred way to carry out the analysis involves using PCR to amplify either the entire TSC1 gene or segments of the gene and then analyzing the amplification products for mutations by single strand conformation polymorphism analysis, heteroduplex analysis, or by direct sequencing of amplified DNA. Methods and primers that have proven successful for the amplification of different regions of TSC1 are described in the Examples section.

For example, exons 9-23 of TSC1 may be amplified using the primers shown in Table 3. The complimentary strands of the amplified exons are then denatured and the individual strands are diluted to allow each molecule to assume a secondary structural conformation. These strands are then subjected to electrophoresis under non-denaturing conditions and the electrophoretic pattern obtained for the sample is compared to the pattern obtained using a control sample obtained from an individual having a normal TSC1 genotype. Any amplification product showing an electrophoretic pattern different from the pattern obtained from the control can then be sequenced to determine the exact mutations present. Additional assays may be performed to determine the amount of hamartin expressed in the cells of a patient, e.g., in cells from biopsy tissue. Assays based upon antibodies such as those described above may be adapted for this purpose.

Although a finding that the TSC1 gene is either under-expressed or mutated suggests that a patient will develop TSC, a finding of normal expression would not necessarily lead to the conclusion that the patient either does not have the disease or will not develop it. Only about half of the patients with a familial form of TSC show linkage indicating an aberration with respect to TSC1 expression. The other half appear to have abnormalities associated with the TSC2 gene. Therefore, it is expected that the present assay will find its greatest effectiveness when combined with assays for TSC2 (see, e.g., WO 95/18226) and used on patients selected for testing either because they have symptoms suggestive of TSC or who come from a family where the disease has been prevalent.

V. Method of Treating or Preventing Abnormal Cellular Proliferation Using TSC1

The characteristics of the TSC1 gene product, i.e., hamartin, indicate that it falls into the category of proteins termed “tumor suppressors.” Mutations resulting in a loss of function of these proteins are associated with tumor formation, and in the case of TSC1, are associated with the development of hamartomas in the brain and other organs. As with other tumor suppressors (see e.g., U.S. Pat. No. 5,532,220), the introduction into cells of DNA expressing the wild-type TSC1 sequence provides a means for inhibiting abnormal, uncontrolled cellular growth. The preferred method for accomplishing this is by operably linking DNA encoding hamartin to a promoter that is active in eukaryotic cells, e.g., the CMV early promoter, and introducing this construct into cells by means of a recombinant retrovirus, e.g., a retrovirus derived from Maloney murine leukemia virus. Standard techniques for the production of appropriate retroviral vectors have been described in the art (see e.g., U.S. Pat. No. 5,532,220).

Although the introduction of DNA encoding hamartin is most clearly relevant to the treatment of patients with TSC caused by mutations in TSC1, it is expected that the present techniques will have application in the control of abnormal cellular growth in other patients as well. Thus, the method may find application in the treatment of patients with a tendency to form polyps, or who have a variety of neoplasms.

VI. Uses of the Present Invention

The utility of certain aspects of the present invention should be readily apparent from the discussion above. Methods for diagnosing TSC and counseling individuals that come from families where the disease is prevalent is of clear value in clinical medicine. The TSC1 gene can be used to provide fragments, controls, and primers for use in such assays and has independent value in ascertaining the levels at which TSC1 is being expressed in patients and in the treatment of abnormal cellular growth.

In addition to diagnostic and therapeutic methods based upon the TSC1 gene and mutated forms of the gene, such methods may also be based upon the gene product, i.e.,. the hamartin protein. For example, the protein may be directly assayed to determine whether its levels are indicative of a normal individual or one likely to develop symptoms characteristic of TSC. Such analyses can probably best be performed using antibody-based assays such as those described above in section III. Thus, the hamartin protein can be used to generate antibodies useful in diagnostic assays. Beyond this, monoclonal antibodies binding only to forms of hamartin containing mutations associated with TSC1, may form the basis of alternative diagnostic procedures. The hamartin protein may be used in the development of appropriate antibodies as well as a control in such assays.

EXAMPLES

I. Methods

Patients

Patients used in the present study were diagnosed as having tuberous sclerosis according to standard diagnostic criteria (Kwiatkowski, et al., Arch Dermatol. 130:348-354 (1994); Roache, et al., J. Child Neruol. 7:221-224 (1992)). Blood samples were obtained after informed consent (approved by local human research committee), and used either directly or after the creation of immortalized Epstein-Barr virus transformed lymphoblastoid cell lines, for the preparation of DNA by standard methods. Families were considered to demonstrate linkage to the TSC1 region if they: 1) demonstrated obligate recombination with markers within 2 cM of the TSC2 gene; and 2) had positive lod scores after analysis with DNA markers from the chromosome 9q34 region (see FIG. 1). Each of the three families used to identify critical recombination events have been previously described (Haines, et al. Am. J. Hum. Genet. 49:764-772 (1991); Nellist, et al., J. Med. Genet. 30:224-227 (1993); Au, et al., Am. J. Path. 149:1201-1208 (1996)). Families providing critical recombinant events were analyzed using multiple markers from the 9q34 region, and haplotype analysis was performed manually to identify the site of recombination.

Gene Identification and Other Methods

Exon trapping was performed according to standard methods and as described previously (Buckler, et al., Proc. Nat'l Acad. Sci. USA 88:4005-4009 (1991); Henske, et al., Am. J. Hum. Genet. 59:400-406 (1996)). Briefly, cosmid, BAC or PAC was digested with PstI or BamHI, and a library of subclones prepared in the pSPL3 vector. This library was then electroporated into cos cells, RNA was collected two days later, RT-PCR performed, a library of exon fragments prepared in the plasmid pGEMblue, and selected clones sequenced. Exons identified in this manner were used to: 1) screen cDNA libraries by conventional methods; 2) screen Genbank and dbEST databases; and 3) used in RT-PCR experiments, all to identify cDNA clones. Image clones were obtained from Research Genetics or the UK HGMP Resource Centre.

cDNA selection was performed using the end ligation coincident sequence cloning method as described by Brookes, et al., Hum. Mol. Genet. 3:2011-2017 (1994). A normalized infant brain cDNA library (Soares, et al., Proc. Nat'l. Acad. Sci. USA 91:9228-9232 (1994)) was screened using whole cosmids as probes by standard methods. A human fetal brain cDNA library (Clontech) was screened by standard phage plating and filter lift methods.

5′ RACE was performed using the Marathon cDNA kit (Clontech), with oligonucleotides derived from B2 cDNA clones, or inferred by analysis of genomic sequence information using the GRAIL program (Xu, et al., Genomics 27:475-480 (1995)). RACE and other cDNA clones were sequenced fully on both strands using Taq cycle sequencing methodology and labeling with ³²P followed by autoradiography, or using an ABI automated sequencer according to standard protocols.

Pulsed field gel electrophoresis was performed to analyze large DNA fragments as described previously (Consortium, Cell 75:1305-1315 (1993)). MluI digestion of DNA embedded in agarose plugs was followed by electrophoresis in a CHEF DRII apparatus and then transferred to nylon filters. Southern blotting for analysis of smaller DNA fragments (1-20 kb) was performed according to standard methods. Probes were labeled with ³²P by random priming in the presence of ³²PdGTP, and hybridization and rinsing were performed at 65° C. in 0.6 M and 60 mM NaCl buffers respectively.

Northern blot analysis was performed by conventional methods using multiple tissue Northern blots (Clontech).

Hybrid Methods

A panel of hybrid cell lines was established to permit analysis of the TSC1 mutation-bearing chromosome 9. 15 TSC families with lod scores greater than 1, with TSC1 region markers and negative linkage with TSC2 region markers were selected for these experiments. The Chinese hamster ovary cell line CHO-K1, which is GAT-, i.e., requires glycine, adenine and thymidine for growth (Kao, et al., Proc. Nat'l Acad. Sci USA 60:1275-1281 (1968)) was fused to lymphoblastoid cell lines derived from TSC patients and hybrids retaining chromosome 9 were selected in growth medium lacking glycine (Fournier, et al. Somat. Cell Genet. 9:69-84 (1983)). Hybrids with retention of chromosome 9 bearing the affected TSC1 allele were identified by analysis with TSC1 region markers (FIG. 1) and used for analysis by PCR.

Genomic Sequencing and Data Management

Approximately 36 cosmids covering 1.2 Mb on 9q34 were chosen to represent a minimal tiling path across the region based upon EcoRI restriction fingerprints (Horniglov, et al., Genomics 41:385-389 (1997)). Cosmid DNA was sheared using a Fisher Scientific 550 Dismemberator Sonicator, and repaired using Mung Bean nuclease (New England Biolabs, Beverly, Mass.), size selected by 2 rounds of agarose gel electrophoresis, and fragments from 1.5-2.5 kb were excised and ligated into SmaI cut M13mp18. After transformation into XL2Blue and plating, single clear plaques were picked using an automated picking device (PBA Technologies, Cambridge, UK), expanded with JM101, and phage supernatant collected. M13 DNA isolation was performed using the Sequatron Robotic system (Hawkins, et al., Science, in press (1997)) following the solid-phase reversible immobilization protocol (Hawkins, et al., Nucl. Acids Res. 22:4543-4544 (1994)). Dye primer DNA sequencing used energy transfer (ET) primers and thermosequenase (Amersham, Chicago, Ill.). After thermal cycling, the reactions were pooled and precipitated with ethanol, resuspended, heated and loaded onto an Applied Biosystems 377 DNA Sequencer.

Once approximately tenfold coverage was attained per cosmid (typically 1200 reads) the gel files were extracted, signal processed and basecalled using Trout (a UNIX based gel analysis package available at ftp from genome.wi.mit.edu/distribution/software/trout) and then assembled using Alewife, a sequence assembly package. Typically, the sequencing reads from a single cosmid assembled into 1-3 contigs, which were then finished by directed primer walking, and directed selection of reverse reads from existing M13 templates to span sequence gaps. Finally, completed projects were analyzed for common repeats entomologies to existing database entries and submitted to GenBank.

Analysis of Genomic Sequence and Mutation Analysis

Genomic sequence was analyzed using the program GRAIL2 to identify possible exons and gene models. Putative transcriptional units were also identified by BLAST searches of public databases and comparison with our own collection of cDNA clones and exon trapping products. These were confirmed by RT-PCR experiments in most cases. Known or putative exons identified by these techniques were analyzed for mutations.

A screening set of 60 DNA samples, 20 from patients from families with linkage to 9q34 and 40 from sporadic patients, was used. Oligonucleotide primers were designed to be external to exons by 40-60 bp, and following application on the screening set, DNAs were analyzed for heteroduplex formation using weak denaturing gels (Couch, et al., Nat. Genet. 13:123-126 (1996); Ganguly, et al., Proc. Nat'l Acad. Sci USA 90:10325-10329 (1993)). Briefly, following amplification, PCR products were heated to 95° C. for 5 minutes, and then incubated at 65° C. for 1 hour. Samples were mixed with 30% formamide and 20% ethylene glycol and immediately loaded on large (35×45 cm) 6% polyacrylamide gels (29:1 acrylamide:bis), containing 15% formamide and 10% ethylene glycol, using an 89 mM tris, 15 mM taurine, 0.5 mM EDTA gradient buffer. After electrophoresis for 2-6 hours, gels were stained with 1 mg/ml ethidium bromide for 5 minutes, rinsed with water, and visualized with 300 nm UV light. Similar techniques were also used for smaller (20 cm×30 cm) gels in some cases. DNA products with mobility shifts were subjected to sequence analysis of both strands, as described above. Some products were subcloned into plasmid vectors to facilitate analysis of individual alleles.

Single strand conformation polymorphism (SSCP) gels were also used to search for mutations, after the initial screening. These were generally run in 1× TBE, using 10% acrylamide gels (37.5:1 acrylamide:bis), under two conditions for 16 cm gels: 20° C. at 400 V for 4 hours, and 4° C. at 100 V for 16 hours. Pre-digestion with Sau3A and/or HinfI was used for longer PCR products in some cases. DNA fragments were visualized by silver staining or through use of ³²P to label PCR products and autoradiography. PCR products with abnormally migrating bands were subjected to sequence analysis.

II. Results

Defining the TSC1 Critical Region

FIG. 1 illustrates the consensus critical region to which TSC1 has been localized (Au, et al., Am. J. Path. 149:1201-1208 (1996); Povey, et al., Ann. Hum. Genet. pp. 9-11 (April, 1994)). The limiting centromeric and telomeric markers are based upon analysis of affected individuals (solid arrows at bottom) from families with individual lod scores of 2 and 4, respectively. These limits are also consistent with LOH studies which have shown the occurrence of LOH for 9q34 markers in 10 of 158 hamartomas from TSC patients, with identification of D9S149 as the proximal limit of LOH in 3 lesions, and D9S298 as the distal limit in 2 lesions (Henske, et al., Ann. Hum. Genet. (1995); Sepp, et al., J. Med. Genet. 33:962-964 (1996)). Also shown in FIG. 1 are two additional recombination events occurring in unaffected individuals (open arrows), also from families with lod scores of 2 or greater (2.0 and 3.9). In each of these families, two individuals from different generations carried the same recombinant chromosome, and all four individuals were without evidence of TSC after complete clinical exam and radiological study. Since non-penetrance in TSC is rare, we judged these individuals to provide additional positioning information and concentrated our search on the region between D9S2127 and DBH, a 900 kb interval.

Construction of a Cosmid Contig and Screening for Large Deletions

An important preliminary study involved the creation of a contig of cloned material for this region (Hornigold, et al., Genomics 41:385-389 (1997)). YACs proved to have limited value in this effort, and cosmids were used as the primary vehicle for construction of a contig, with filled-in of gaps using P1, PAC, and BAC clones. In a search for further positional information, 5 MluI restriction fragments covering the critical region were assayed in 265 unrelated patients with TSC using PFGE and hybridization to the probes shown in FIG. 1. No abnormalities suggestive of a genomic rearrangement were seen.

We also looked for deletions within the TSC1 region using a panel of 15 hybrid cell lines derived from patients from families with linkage to 9q34 and having a single chromosome 9 bearing the affected TSC1 allele. Analysis of these hybrid cell lines using 22 sets of primers derived from STSs and genes within the candidate region revealed no evidence of partial or complete deletion.

Gene Identification

From the cosmids, 142 exons were identified using exon-trapping methodology in the region between D9S1199 and D9S114. 13 novel genes from the region were identified in this manner (Table 1). Additional genes in the region were identified by cDNA selection methodology and use of cosmid DNA as probes for cDNA libraries. EST clones, mapped to this general genomic region by radiation hybrid mapping, were also mapped to specific cosmids. Several of the genes identified appeared to be good candidates based upon a probable or defined role in signal transduction pathways governing growth regulation. However, analysis of these genes did not reveal any evidence of mutation in patients with TSC.

A transcriptional unit denoted B2 was identified by hybridization of a cosmid containing D9S1830 (FIG. 1) to an arrayed infant brain library. Serial screening of a human fetal brain cDNA library with initial isolates yielded a cDNA clone of size 4.5 kb, which was sequenced and found to contain no open reading frame (ORF). Northern analysis showed a transcript of size 8.6 kb in every tissue tested (see below). Database searches revealed this clone was the 3′ portion of a recently identified 6.8 kb cDNA clone (KIAA 0243, GenBank #D87683) Nagase, et al., DNA Res. 3: 321-329 (1996)), of unknown function with an ORF of 2 kb. This larger clone was obtained and the entire 6.8 kb cDNA was used to screen DNA samples from 150 unrelated TSC patients by Southern analysis after digestion with TaqIPstI HindIII, and EcoRI. No aberrant hybridization patterns were observed.

Genomic Sequencing and Screening for TSC-Associated Mutations

In parallel, we initiated a strategy to sequence the entire contig covering the 900 kb critical region, arguing that additional candidate genes would be discovered by this approach, and that the genomic sequence information would facilitate analysis of exons for mutations. After 208 kb of the genomic sequence of the region had been obtained, we had discovered an additional 4 probable new genes, and partial or complete genomic sequence information was derived for 3 genes identified in previous studies.

Putative exons predicted from the genomic sequence were PCR-amplified in a screening set of 60 DNA samples comprising an affected member of each of 20 unrelated TSC families showing linkage to 9q34 and 40 sporadic TSC cases. Heteroduplex analysis was employed to screen for mutations using weakly denaturing polyacrylamide gels. The 62nd exon screened was part of the previously identified B2 gene and demonstrated mobility shifts in 10 of the 60 patient samples (FIG. 2A). This exon was therefore subjected to detailed analysis.

Analysis of the Exon with Mobility Shifts

Sequencing of the amplified products associated with mobility shifts on heteroduplex analysis revealed 7 small frameshifting deletions (3 of which were identical), one nonsense mutation, one missense change, and one polymorphism which did not change the encoded amino acid (FIG. 2B, Table 2). Eight of the 9 mutations identified were from the 20 familial cases tested, with only one mutation seen among the 40 sporadic cases (FIG. 2C). Analysis of samples from other family members confirmed that each of the familial mutations segregated with TSC and that a frameshift mutation had occurred de novo in the sporadic case (FIG. 2D).

Haplotype analysis using markers flanking this exon (D9S2126, D9S1830, D9S1199) indicated that the recurrent mutation, 2105 deLAAg, had occurred independently in 3 unrelated families, 2 polish and I American. These data showed that gene B2 was likely the TSC1 gene and further studies were undertaken to determine its structure and sequence.

The Complete Sequence and Structure of the TSC1 Gene

The 5′ portion of the TSC1 gene was identified by 5′ RACE. Some RACE clones had internal deletions when compared to the longest sequence obtained (FIG. 4). Oligonucleotide primers designed from these variably retained regions (bp 49-77 and bp 78-140) hybridized to distinct EcoRI fragments in cosmids telomeric to D9S 1830, and comparison with other mapping studies indicated that they were located 5′ to the remainder of the gene (bp 200-8600). This suggested that the regions represented variably spliced exons.

The open reading frame of the longest transcript begins at b162 with the first ATO codon at residue 222. Other methionine residues are found downstream in the same reading frame at positions 258 and 273. Translation may initiate at the first of these methionines, since it matches the Kozak consensus sequence for translation initiation (Kozak, Nucl. Acids Res. 15:(1987)). All three potential initiator methionines are 3′ of the variable, presumably alternatively spliced, region and there is a 3′ untranslated region of approximately 4.5 kb (see SEQ ID NO:1). Northern blot analysis with a coding region probe (bp 1100-2100) demonstrated a major 8.6 kb message that was widely expressed and that was particularly abundant in skeletal muscle (FIG. 3). The genomic structure of the TSC1 gene is shown in FIG. 5 and Table 3.

The predicted TSC1 protein, hamartin, is 1164 amino acid residues in length with a calculated mass of 130 kDa. The protein is generally hydrophilic and has a single potential transmembrane domain at amino acid residues 127-144 (Smith, et al., Genome Res. 6:454-462 (1996)). Database searches identified a possible homologue of TSC1 in the yeast Schizosaccharomyces pombe (GenBank #q09778), a hypothetical protein of Mw 103 kDa. There were no strong matches with known vertebrate proteins. Hamartin contains a potential coiled-coil region of 266 amino acids beginning at position 730 (Lupas, et al., Science 252:1162-1164 (1991)).

Other Mutations Found in TSC1

Because a high frequency of exon 15 mutations were identified in initial screens, we studied this exon in a larger sample of TSC patients. Mutations in exon 15 (559 bp, 16% coding region) were identified in 8 of 55 (15%) familial DNA samples, and in 15 of 607 (2.5%) of DNA samples from sporadic patients or unlinked families (Table 4). A screen for mutations in all coding exons in 20 familial cases and 152 sporadic patients yielded 8 mutations in each group (40% and 5%, respectively). In total, 19 mutations were found in coding exons other than exon 15. No mutations have been detected thus far in exons 3-6, 8, 11-14, 16 or 21-23. Of the 32 distinct mutations seen in 42 different patients/families, 5 were observed more than once. Thirty were predicted to be truncating, one was a missense mutation, and one was a splice site mutation.

Analysis of TSC Lesions Provides Evidence of the Tumor Suppressor Function of TSC1

Analysis of DNA from a renal cell carcinoma from a patient with germline mutation 2105delAAAG, revealed a somatic mutation, 1957delG, in the wild-type TSC1 allele. A giant cell astrocytoma from another patient with a germline 1942delGGinsTTGA mutation had retained the mutant allele but lost the wild-type allele. These results suggest that the wild-type TSC1 gene has the characteristics of a tumor suppressor.

TABLE 1 Genes Found in the TSC1 Critical Region Coding Gene region mRNA size Expression Function A 2 kb 3 kb ubiquitous guanine nucleotide binding protein VAV2 2.7 kb 4 kb ubiquitous guanine nucleotide exchange factor DMGdh 3 kb ND liver dimethlglycine dehydrogenase B1 >0.2 kb ND ND unknown E >0.4 kb 3 kb brain, liver, unknown kidney kB2 >2.3 kb 4 kb ubiquitous thrombospondin homology D 0.7 kb 2.6 kb ubiquitous unknown C >1.5 kb 4.5 kb liver unknown 6f >0.6 kb ND ND unknown 3f >0.6 kb ND ND unknown XPMC2H 1.2 kb 2.5 kb ubiquitous mitotic regulation (?) RALGDS 2.7 kb 4.0 kb ubiquitous guanine nucleotide exchange factor 9b9b 1.5 kb 2.0 kb ubiquitous unknown A9 B2 2 kb 8.5 kb ubiquitous unknown B11 4 kb ND ND unknown C10 0.6 kb ND ND unknown GR1 0.9 kb ND ND adenylate kinase GR2 1.3 kb ND ND growth factor inhibitor GR3 >0.8 kb ND ND unknown GR4 2.3 kb ND ND sugar transporter homology ND, not done.

TABLE 2 Mutations in TSC1 Found in Initial Screening Number UPN Mutation affected Mutation Effect MF24-1 1746C−>T 4 truncation MF12-1 1981A−>G 8 K585R MF6-1 2041delTT 4 truncation MF3-1 2105delAAAG 4 truncation Pol42-1 2105delAAAG 2 truncation Pol74-1 2105delAAAG 3 truncation MS91-1 2122delAC 1 truncation MF11-1 2126delAG 4 truncation MF14-1 2176delTG 7 truncation

TABLE 3 Genomic Structure of the TSC1 Gene and Primers Used for PCR Analysis Exon cDNA bp Size Genomic bp Primers SEQ ID NO  9  959-1134 176   718-893   ccagagacaaagttgcaaaacag; 3 ttgattacagtttgcatttcttgac 4 10 1135-1250 116  1606-1721  aaagcagaggagagagcagg; 5 cctaaaaccacacactaacccc 6 11 1251-1362 112  2061-2172  aaggcaggccaaaaccaac; 7 tgacttagcattcctttgccac 8 12 1363-1484 122  2482-2603  agtgagtcactgtgcctgg; 9 tgttctgcccttgtctctaag 10 13 1485-1554 70  5804-5873  ccaattagaagaggcaagc; 11 gcaacatttttcgtcttgtg 12 15 1660-2218 559  7035-7593  gagagtgccccagtcccttac; 13 ccaggtggaataccgactgc 14 16 2219-2262 44  8720-8763  tggatttggagctaaagtaacaac; 15 cgtttttttcttggtaagatcg 16 17 2263-2429 167  9357-9523  tcatgctgacccaaaacaaaac; 17 aaaggcatttctgccaccc 18 18 2430-2612 183 10387-10569 actgactgcctccctcccc; 19 tcgcagtgtgtgttaaattgcc 20 19 2613-2723 111 11475-11585 acctgtctgaaggaagaatgttag; 21 cctcaaacttcatgtccacg 22 20 2724-2846 123 12337-12459 actgtctgggtctgaaacgc; 23 tttatgtcgtcggatttttcac 24 21 2847-3034 188 15566-15753 cacagtccttatgctggaattg; 25 tttttttcaggaagtagaaatgatg 26 22 3035-3196 162 15831-15992 cacagtccttatgctggaattg; 25 tttttttcaggaagtagaaatgatg 26 23 3197-8600 5404 16422-21825 cctcctgttctgtgccaac; 27 tcaccagctccttttttcctc 28 Note: Exons 21 and 22 were amplified as a single PCR product.

TABLE 4 All Mutations Found in TSC1 # Patients Screened - Exon familial (F)/other (S) Mutations Patients 7 20F/152S 865delTT 1S 9 39F/230S 966delA 1S 97OT−>G,L250X 1F 993G−>T,E258X 1F 1112T−>G,Y297X 1F 10 20F/152S 1207delCT 1S 15 55F/607S 1746C−>T,R509X 2S, 1F 1750delCA 1S 1801delAG 1F 1892del23 1S 1929delAG 2S 1942delGGinsTTGA 1S 1981A−>G,K585R 1F 2009delT 1S 2041delTT 1F 2060delA 1S 2105delAAAG 4F, 2S 2122delAC 1S 2126delAG 1F, 1S 2176delTG 1F 17 45F/296S 2295C−>T,R692X 1F 2324duplGTTACTC 1S 2332delAT 1S 2395insA 1S 18 45F/296S 2448C−>T,Q743X 1S 2519del23bp 1S 2540delC 1F 2577C−>T,R786X 1F, 1S 2583G−>T,E788X 1F 19 39F/230S 2691delAC 1S 20 39F/230S 2724-1G−>T 1F 2730insA 1S 1Families with linkage to the TSC1 region and negative linkage to the TSC2 region (F); others (S) include both sporadic cases, and those from families without linkage information. See methods for further details.

III. Discussion

The TSC1 gene has been identified using a conventional positional cloning approach supplemented with genomic sequencing. Employing a mutation screening strategy scanning all possible exons, an exon from a recently identified gene of unknown function was found to contain several mutations in TSC patient DNA samples. The full genomic sequence of the TSC1 gene is presented and distinct mutations in apparently unrelated patients/families have been identified.

Based upon the studies discussed herein, the mutational spectrum of the TSC1 locus mainly comprises small deletions, small insertions, and point mutations which, in the majority of cases, are likely to inactivate protein function. This restricted mutational spectrum may reflect an intrinsic tendency for these types of mutations to occur in this region of the genome, or, alternatively, the strong negative survival effect of more disruptive mutations such as large deletions. Negative effects from large deletions are certainly possible given the high gene density near the TSC1 locus.

The results support the hypothesis that TSC1 functions as a tumor suppressor gene. First, the majority of mutations seen thus far are inactivating. Second, in two TSC associated tumors, there was loss of the wild-type TSC1 allele through loss of heterogeneity (LOH) or intragenic somatic mutation. The paucity of LOH for the TSC1 region among patient lesions examines today (Carbonara, et al., Cancer 15:18-25 (1996); Sepp, et al., J. Med. Genet. 33:962-964 (1996)) may reflect the same mutational spectrum seen in the germline of TSC patients with a high frequency of small mutations causing inactivation of the second allele and/or a greater frequency of TSC2 involvement in the populations under study.

The TSC1 gene encodes a 1164 amino acid protein, termed hamartin which is generally hydrophilic and which contains a putative coiled-coil domain which is a potential site of protein-protein interaction. The specific biochemical mechanism by which loss of hamartin expression leads to development of TSC lesions is unknown. It is likely that hamartin and tuberin, the product of the TSC2 gene, participate in the same pathway of cellular growth control, since the clinical features of TSC due to the two genes are so similar. The sequence homology of hamartin to a putative S pombe protein suggests that these proteins may participate in an evolutionarily conserved pathway of eukaryotic growth regulation. The identification of TSC1 will enable further analysis of the functions of these proteins, which will be important in unraveling the molecular pathogenesis of TSC.

All references cited are fully incorporated by reference. Having now fully described the invention, it will be understood by those of skill in the art that the invention may be performed within a wide and equivalent range of conditions, parameters, and the like, without affecting the spirit or scope of the invention or any embodiment thereof.

28 8600 base pairs nucleic acid double linear cDNA NO NO 1 GTGCTGTACG TCCAAGATGG CGGCGCCTGT AGGCTGGAGG GACTGTGAGG TAAACAGCTG 60 AGGGGGAGGA GACGGTGGTG ACCATGAAAG ACACCAGGTT GACAGCACTG GAAACTGAAG 120 TACCAGTTGT CGCTAGAACA GTTTGGTAGT GGCCCCAATG AAGAACCTTC AGAACCTGTA 180 GCACACGTCC TGGAGCCAGC ACAGCGCCTT CGAGCGAGAG AATGGCCCAA CAAGCAAATG 240 TCGGGGAGCT TCTTGCCATG CTGGACTCCC CCATGCTGGG TGTGCGGGAC GACGTGACAG 300 CTGTCTTTAA AGAGAACCTC AATTCTGACC GTGGCCCTAT GCTTGTAAAC ACCTTGGTGG 360 ATTATTACCT GGAAACCAGC TCTCAGCCGG CATTGCACAT CCTGACCACC TTGCAAGAGC 420 CACATGACAA GCACCTCTTG GACAGGATTA ACGAATATGT GGGCAAAGCC GCCACTCGTT 480 TATCCATCCT CTCGTTACTG GGTCATGTCA TAAGACTGCA GCCATCTTGG AAGCATAAGC 540 TCTCTCAAGC ACCTCTTTTG CCTTCTTTAC TAAAATGTCT CAAGATGGAC ACTGACGTCG 600 TTGTCCTCAC AACAGGCGTC TTGGTGTTGA TAACCATGCT ACCAATGATT CCACAGTCTG 660 GGAAACAGCA TCTTCTTGAT TTCTTTGACA TTTTTGGCCG TCTGTCATCA TGGTGCCTGA 720 AGAAACCAGG CCACGTGGCG GAAGTCTATC TCGTCCATCT CCATGCCAGT GTGTACGCAC 780 TCTTTCATCG CCTTTATGGA ATGTACCCTT GCAACTTCGT CTCCTTTTTG CGTTCTCATT 840 ACAGTATGAA AGAAAACCTG GAGACTTTTG AAGAAGTGGT CAAGCCAATG ATGGAGCATG 900 TGCGAATTCA TCCGGAATTA GTGACTGGAT CCAAGGACCA TGAACTGGAC CCTCGAAGGT 960 GGAAGAGATT AGAAACTCAT GATGTTGTGA TCGAGTGTGC CAAAATCTCT CTGGATCCCA 1020 CAGAAGCCTC ATATGAAGAT GGCTATTCTG TGTCTCACCA AATCTCAGCC CGCTTTCCTC 1080 ATCGTTCAGC CGATGTCACC ACCAGCCCTT ATGCTGACAC ACAGAATAGC TATGGGTGTG 1140 CTACTTCTAC CCCTTACTCC ACGTCTCGGC TGATGTTGTT AAATATGCCA GGGCAGCTAC 1200 CTCAGACTCT GAGTTCCCCA TCGACACGGC TGATAACTGA ACCACCACAA GCTACTCTTT 1260 GGAGCCCATC TATGGTTTGT GGTATGACCA CTCCTCCAAC TTCTCCTGGA AATGTCCCAC 1320 CTGATCTGTC ACACCCTTAC AGTAAAGTCT TTGGTACAAC TGCAGGTGGA AAAGGAACTC 1380 CTCTGGGAAC CCCAGCAACC TCTCCTCCTC CAGCCCCACT CTGTCATTCG GATGACTACG 1440 TGCACATTTC ACTCCCCCAG GCCACAGTCA CACCCCCCAG GAAGGAAGAG AGAATGGATT 1500 CTGCAAGACC ATGTCTACAC AGACAACACC ATCTTCTGAA TGACAGAGGA TCAGAAGAGC 1560 CACCTGGCAG CAAAGGTTCT GTCACTCTAA GTGATCTTCC AGGGTTTTTA GGTGATCTGG 1620 CCTCTGAAGA AGATAGTATT GAAAAAGATA AAGAAGAAGC TGCAATATCT AGAGAACTTT 1680 CTGAGATCAC CACAGCAGAG GCAGAGCCTG TGGTTCCTCG AGGAGGCTTT GACTCTCCCT 1740 TTTACCGAGA CAGTCTCCCA GGTTCTCAGC GGAAGACCCA CTCGGCAGCC TCCAGTTCTC 1800 AGGGCGCCAG CGTGAACCCT GAGCCTTTAC ACTCCTCCCT GGACAAGCTT GGGCCTGACA 1860 CACCAAAGCA AGCCTTTACT CCCATAGACC TGCCCTGCGG CAGTGCTGAT GAAAGCCCTG 1920 CGGGAGACAG GGAATGCCAG ACTTCTTTGG AGACCAGTAT CTTCACTCCC AGTCCTTGTA 1980 AAATTCCACC TCCGACGAGA GTGGGCTTTG GAAGCGGGCA GCCTCCCCCG TATGATCATC 2040 TTTTTGAGGT GGCATTGCCA AAGACAGCCC ATCATTTTGT CATCAGGAAG ACTGAGGAGC 2100 TGTTAAAGAA AGCAAAAGGA AACACAGAGG AAGATGGTGT GCCCTCTACC TCCCCAATGG 2160 AAGTGCTGGA CAGACTGATA CAGCAGGGAG CAGACGCGCA CAGCAAGGAG CTGAACAAGT 2220 TGCCTTTACC CAGCAAGTCT GTCGACTGGA CCCACTTTGG AGGCTCTCCT CCTTCAGATG 2280 AGATCCGCAC CCTCCGAGAC CAGTTGCTTT TACTGCACAA CCAGTTACTC TATGAGCGTT 2340 TTAAGAGGCA GCAGCATGCC CTCCGGAACA GGCGGCTCCT CCGCAAGGTG ATCAAAGCAG 2400 CAGCTCTGGA GGAACATAAT GCTGCCATGA AAGATCAGTT GAAGTTACAA GAGAAGGACA 2460 TCCAGATGTG GAAGGTTAGT CTGCAGAAAG AACAAGCTAG ATACAATCAG CTCCAGGAGC 2520 AGCGTGACAC TATGGTAACC AAGCTCCACA GCCAGATCAG ACAGCTGCAG CATGACCGAG 2580 AGGAATTCTA CAACCAGAGC CAGGAATTAC AGACGAAGCT GGAGGACTGC AGGAACATGA 2640 TTGCGGAGCT GCGGATAGAA CTGAAGAAGG CCAACAACAA GGTGTGTCAC ACTGAGCTGC 2700 TGCTCAGTCA GGTTTCCCAA AAGCTCTCAA ACAGTGAGTC GGTCCAGCAG CAGATGGAGT 2760 TCTTGAACAG GCAGCTGTTG GTTCTTGGGG AGGTCAACGA GCTCTATTTG GAACAACTGC 2820 AGAACAAGCA CTCAGATACC ACAAAGGAAG TAGAAATGAT GAAAGCCGCC TATCGGAAAG 2880 AGCTAGAAAA AAACAGAAGC CATGTTCTCC AGCAGACTCA GAGGCTTGAT ACCTCCCAAA 2940 AACGGATTTT GGAACTGGAA TCTCACCTGG CCAAGAAAGA CCACCTTCTT TTGGAACAGA 3000 AGAAATATCT AGAGGATGTC AAACTCCAGG CAAGAGGACA GCTGCAGGCC GCAGAGAGCA 3060 GGTATGAGGC TCAGAAAAGG ATAACCCAGG TGTTTGAATT GGAGATCTTA GATTTATATG 3120 GCAGGTTGGA GAAAGATGGC CTCCTGAAAA AACTTGAAGA AGAAAAAGCA GAAGCAGCTG 3180 AAGCAGCAGA AGAAAGGCTT GACTGTTGTA ATGACGGGTG CTCAGATTCC ATGGTAGGGC 3240 ACAATGAAGA GGCATCTGGC CACAACGGTG AGACCAAGAC CCCCAGGCCC AGCAGCGCCC 3300 GGGGCAGTAG TGGAAGCAGA GGTGGTGGAG GCAGCAGCAG CAGCAGCAGC GAGCTTTCTA 3360 CCCCAGAGAA ACCCCCACAC CAGAGGGCAG GCCCATTCAG CAGTCGGTGG GAGACGACTA 3420 TGGGAGAAGC GTCTGCCAGC ATCCCCACCA CTGTGGGCTC ACTTCCCAGT TCAAAAAGCT 3480 TCCTGGGTAT GAAGGCTCGA GAGTTATTTC GTAATAAGAG CGAGAGCCAG TGTGATGAGG 3540 ACGGCATGAC CAGTAGCCTT TCTGAGAGCC TAAAGACAGA ACTGGGCAAA GACTTGGGTG 3600 TGGAAGCCAA GATTCCCCTG AACCTAGATG GCCCTCACCC GTCTCCCCCG ACCCCGGACA 3660 GTGTTGGACA GCTACATATC ATGGACTACA ATGAGACTCA TCATGAACAC AGCTAAGGAA 3720 TGATGGTCAA TCAGTGTTAA CTTGCATATT GTTGGCACAG AACAGGAGGT GTGAATGCAC 3780 GTTTCAAAGC TTTCCTGTTT CCAGGGTCTG AGTGCAAGTT CATGTGTGGA AATGGGACGG 3840 AGGTCCTTTG GACAGCTGAC TGAATGCAGA ACGGTTTTTG GATCTGGCAT TGAAATGCCT 3900 CTTGACCTTC CCCTCCACCC GCCCTAACCC CCTCTCATTT ACCTCGCAGT GTGTTCTAAT 3960 CCAAGGGCCA GTTGGTGTTC CTCAGTAGCT TTACTTTCTT CCTTCCCCCC CAAATGGTTG 4020 CGTCCTTTGA ACCTGTGCAA TATGAGGCCA AATTTAATCT TTGAGTCTAA CACACCACTT 4080 TCTGCTTTCC CGAAGTTCAG ATAACTGGGT TGGCTCTCAA TTAGACCAGG TAGTTTGTTG 4140 CATTGCAGGT AAGTCTGGTT TTGTCCCTTC CAGGAGGACA TAGCCTGCAA AGCTGGTTGT 4200 CTTTACATGA AAGCGTTTAC ATGAGACTTT CCGACTGCTT TTTTGATTCT GAAGTTCAGC 4260 ATCTAAAGCA GCAGGTCTAG AAGAACAACG GTTTATTCAT ACTTGCATTC TTTTGGCAGT 4320 TCTGATAAGC TTCCTAGAAA GTTCTGTGTA AACAGAAGCC TGTTTCAGAA ATCTGGAGCT 4380 GGCACTGTGG AGACCACACA CCCTTTGGGA AAGCTCTTGT CTCTTCTTCC CCCACTACCT 4440 CTTATTTATT TGGTGTTTGC TTGAATGCTG GTACTATTGT GACCACAGGC TGGTGTGTAG 4500 GTGGTAAAAC CTGTTCTCCA TAGGAGGGAA GGAGCAGTCA CTGGGAGAGG TTACCCGATA 4560 AGCACTTGAG CATGAGGAAC TGCACCTTTA GGCCATCTCA GCTTGCTGGG CCTTTTGTTA 4620 AACCCTTCTG TCTACTGGCC TCCCTTTGTG TGCATACGCC TCTTGTTCAT GTCAGCTTAT 4680 ATGTGACACT GCAGCAGAAA GGCTCTGAAG GTCCAAAGAG TTTCTGCAAA GTGTATGTGA 4740 CCATCATTTC CCAGGCCATT AGGGTTGCCT CACTGTAGCA GGTTCTAGGC TACCAGAAGA 4800 GGGGCAGCTT TTTCATACCA ATTCCAACTT TCAGGGGCTG ACTCTCCAGG GAGCTGATGT 4860 CATCACACTC TCCATGTTAG TAATGGCAGA GCAGTCTAAA CAGAGTCCGG GAGAATGCTG 4920 GCAAAGGCTG GCTGTGTATA CCCACTAGGC TGCCCCACGT GCTCCCGAGA GATGACACTA 4980 GTCAGAAAAG TGGCAGTGGC AGAGAATCCA AACTCAACAA GTGCTCCTGA AAGAAATGCT 5040 AGAAGCCTAA GAACTGTGGT CTGGTGTTCC AGCTGAGGCA GGGGGATTTG GTAGGAAGGA 5100 GCCAGTGAAC TTGGCTTTCC TGTTTCTATC TTTCATTAAA AAGAATAGAA GGATTCAGTC 5160 ATAAAGAGGT AAAAAACTGT CACGGTACGA AATCTTAGTG CCTACGGAGG CCTCGAGCAG 5220 AAAGAATGAA AGTCTTTTTT TTTTTTTTTT TTTTTTAGCA TGGCAATAAA TATTCTAGCA 5280 TCCCTAACTA AAGGGGACTA GACAGTTAGA GACTCTGTCA CCCTAGCTAT ACCAGCAGAA 5340 AACCTGTTCA GGCAGGCTTT CTGGGTGTGA CTGATTCCCA GCCTGTGGCA GGGCGTGGTC 5400 CCAACTACTC AGCCTAGCAC AGGCTGGCAG TTGGTACTGA ATTGTCAGAT GTGGAGTATT 5460 AGTGACACCA CACATTTAAT TCAGCTTTGT CCAAAGGAAA GCTTAAAACC CAATACAGTC 5520 TAGTTTCCTG GTTCCGTTTT AGAAAAGGAA AACGTGAACA AACTTAGAAA GGGAAGGAAA 5580 TCCCATCAGT GAATCCTGAA ACTGGTTTTA AGTGCTTTCC TTCTCCTCAT GCCCAAGAGA 5640 TCTGTGCCAT AGAACAAGAT ACCAGGCACT TAAAGCCTTT TCCTGAATTG GAAAGGAAAA 5700 GAGGCCCAAG TGCAAAAGAA AAAACATTTT AGAAACGGAC AGCTTATAAA AATAAAGGGA 5760 AGAAAGGAGG CAGCATGGAG AGAGGCCTGT GCTAGAAGCT CCATGGACGT GTCTGCACAG 5820 GGTCCTCAGC TCATCCATGC GGCCTGGGTG TCCTTTTACT CAGCTTTATA ACAAATGTGG 5880 CTCCAAGCTC AGGTGCCTTT GAGTTCTAGG AGGCTGTGGG TTTTATTCAA CTACGGTTGG 5940 GAGAATGAGA CCTGGAGTCA TGTTGAAGGT GCCCAACCTA AAAATGTAGG CTTTCATGTT 6000 GCAAAGAACT CCAGAGTCAG TAGTTAGGTT TGGTTTGGTT TTGGACATGA TAAACCTGCC 6060 AAGAGTCAAC AGGTCACTTG ATCATGCTGC AGTGGGTAGT TCTAAGGATG GAAAGGTGAC 6120 AGTATTACTC TCGAGAGGCA ATTCAGTCCT GGGCAAAGGT ATTAGTACAA TAAGCGTTAA 6180 GGGCAGAGTC TACCTTGAAA CCAATTAAGC AGCTTGGTAT TCATAAATAT TGGGATTGGA 6240 TGGCCTCCAT CCAGAAATCA CTATGGGTGA GCATACCTGT CTCAGCTGTT TGGCCAATGT 6300 GCATAACCTA CTCGGATCCC CACCTGACAC TAACCAGAGT CAGCACAGGC CCCGAGGAGC 6360 CCGAAGTTCT CTGCTGTGCA GCATGGAATT CCTTTAAAAA GGTGCACTAC AGTTTTAGCG 6420 GGGAGGGGGA TAGGAAGACG CAGAGCAAAT GAGCTCCGGA GTCCCTGCAG GTGAATAAAC 6480 ACACAGATCT GCATCTGATA GAACTTTGAT GGATTTTCAA AAAGCCGTTG ACAAGGCTCT 6540 GCTATACAGT CTATAAAAAT TGTTATTATG GGATTGGAAG AAACACATGG TCATGAATAG 6600 AAAAAAAACA AACCCAAAGG TAGGAAGGTC AAGGTCATTT CTTAGATGGA GAAGTTGTAG 6660 AAGATGTCCT TGGAGATGAG TTTTAGGACC AGCATTACTA AGGCAGGTGG GCAGACAGTG 6720 ACCTCTCTAG GTGTGTCCAC AGAGTTTTTC AGGAGAGAAA ACTGCCTGAC CTTTGGGACT 6780 AAGCTGCGGA ATCTTCTTAC TAAGCTTGAA GAGTGGAGAG GCGAGAGGTG AGCTACTTTG 6840 TGAGCCAAAG CTTATGTGAC ATGGTTGGGG AAACAGTCCA AACTGTTCTG AGAAGGTGAA 6900 CTGTTACGAC CCAGGACAAT TAGAAAAATT CACCCACCAT GCCGCACATT ACTGGGTAAA 6960 AGCAGGGCAG CAGGGAACAA AACTCCAGAC TCTTGGGCCG TCCCCATTTG CAACAGCACA 7020 CATAGTTTCT GGTATATTTG TTGGGAAAGA TAAAACTCTA GCAGTTGTTG AGGGGAGGAT 7080 GTATAAAATG GTCATGGGGA TGAAAGGATC TCTGAGACCA CAGAGGCTCA GACTCACTGT 7140 TAAGAATAGA AAACTGGGTA TGCGTTTCAT GTAGCCAGCA GAACTGAAGT GTGCTGTGAC 7200 AAGCCAATGT GAATTTCTAC CAAATAGTAG AGCATACCAC TTGAAGAAGG AAAGAACCGG 7260 AGAGCAAACA AAAGTTCTGC GTAATGAGAC TCACCTTTTC TCGCTGAAAG CACTAAGAGG 7320 TGGGAGGAGG CCTGCACAGG CTGGAGGAGG GTTTGGGCAG AGCGAAGACC CGGCCAGGAC 7380 CTTGGTGAGA TGGAGTGCCG CCCACCTCCT GCGGATACTC TTGGAGAGTT GTTCCCCCAG 7440 GGGNCTCTGC CCCACCTGGA GAAGGAAGCT GCCTGGTGTG GAGTGACTCA AATCAGTATA 7500 CCTATCTGCT GCACCTTCAC TCTCCAGGGT ACATGCTTTA AAACCGACCC GCAACAAGTA 7560 TTGGAAAAAT GTATCCAGTC TGAAGATGTT TGTGTATCTG TTTACATCCA GAGTTCTGTG 7620 ACACATGCCC CCCAGATTGC TGCAAAGATC CCAAGGCATT GATTGCACTT GATTAAGCTT 7680 TTGTCTGTAG GTGAAAGAAC AAGTTTAGGT CGAGGACTGG CCCCTAGGCT GCTGCTGTGA 7740 CCCTTGTCCC ATGTGGCTTG TTTGCCTGTC CGGGACTCTT CGATGTGCCC AGGGGAGCGT 7800 GTTCCTGTCT CTTCCATGCC GTCCTGCAGT CCTTATCTGC TCGCCTGAGG GAAGAGTAGC 7860 TGTAGCTACA AGGGAAGCCT GCCTGGAAGA GCCGAGCACC TGTGCCCATG GCTTCTGGTC 7920 ATGAAACGAG TTAATGATGG CAGAGGAGCT TCCTCCCCAC TTCGCAGCGC CACATTATCC 7980 ATCCTCTGAG ATAAGTAGGC TGGTTTAACC ATTGGAATGG ACCTTTCAGT GGAAACCCTG 8040 AGAGTCTGAG AACCCCCAGA CCAACCCTTC CCTCCCTTTC CCCACCTCTT ACAGTGTTTG 8100 GACAGGAGGG TATGGTGCTG CTCTGTGTAG CAAGTACTTT GGCTTATGAA AGAGGCAGCC 8160 ACGCATTTTG CACTAGGAAG AATCAGTAAT CACTTTTCAG AAGACTTCTA TGGACCACAA 8220 ATATATTACG GAGGAACAGA TTTTGCTAAG ACATAATCTA GTTTTATAAC TCAATCATGA 8280 ATGAACCATG TGTGGCAAAC TTGCAGTTTA AAGGGGTCCC ATCAGTGAAA GAAACTGATT 8340 TTTTTTAACG GACTGCTTTT AGTTAAATTG AAGAAAGTCA GCTCTTGTCA AAAGGTCTAA 8400 ACTTTCCCGC CTCAATCCTA AAAGCATGTC AACAATCCAC ATCAGATGCC ATAAATATGA 8460 ACTGCAGGAT AAAATGGTAC AATCTTAGTG AATGGGAATT GGAATCAAAA GAGTTTGCTG 8520 TCCTTCTTAG AATGTTCTAA AATGTCAAGG CAGTTGCTTG TGTTTAACTG TGAACAAATA 8580 AAAATTTATT GTTTTGCACT 8600 1164 amino acids amino acid not relevant not relevant protein NO NO 2 Met Ala Gln Gln Ala Asn Val Gly Glu Leu Leu Ala Met Leu Asp Ser 1 5 10 15 Pro Met Leu Gly Val Arg Asp Asp Val Thr Ala Val Phe Lys Glu Asn 20 25 30 Leu Asn Ser Asp Arg Gly Pro Met Leu Val Asn Thr Leu Val Asp Tyr 35 40 45 Tyr Leu Glu Thr Ser Ser Gln Pro Ala Leu His Ile Leu Thr Thr Leu 50 55 60 Gln Glu Pro His Asp Lys His Leu Leu Asp Arg Ile Asn Glu Tyr Val 65 70 75 80 Gly Lys Ala Ala Thr Arg Leu Ser Ile Leu Ser Leu Leu Gly His Val 85 90 95 Ile Arg Leu Gln Pro Ser Trp Lys His Lys Leu Ser Gln Ala Pro Leu 100 105 110 Leu Pro Ser Leu Leu Lys Cys Leu Lys Met Asp Thr Asp Val Val Val 115 120 125 Leu Thr Thr Gly Val Leu Val Leu Ile Thr Met Leu Pro Met Ile Pro 130 135 140 Gln Ser Gly Lys Gln His Leu Leu Asp Phe Phe Asp Ile Phe Gly Arg 145 150 155 160 Leu Ser Ser Trp Cys Leu Lys Lys Pro Gly His Val Ala Glu Val Tyr 165 170 175 Leu Val His Leu His Ala Ser Val Tyr Ala Leu Phe His Arg Leu Tyr 180 185 190 Gly Met Tyr Pro Cys Asn Phe Val Ser Phe Leu Arg Ser His Tyr Ser 195 200 205 Met Lys Glu Asn Leu Glu Thr Phe Glu Glu Val Val Lys Pro Met Met 210 215 220 Glu His Val Arg Ile His Pro Glu Leu Val Thr Gly Ser Lys Asp His 225 230 235 240 Glu Leu Asp Pro Arg Arg Trp Lys Arg Leu Glu Thr His Asp Val Val 245 250 255 Ile Glu Cys Ala Lys Ile Ser Leu Asp Pro Thr Glu Ala Ser Tyr Glu 260 265 270 Asp Gly Tyr Ser Val Ser His Gln Ile Ser Ala Arg Phe Pro His Arg 275 280 285 Ser Ala Asp Val Thr Thr Ser Pro Tyr Ala Asp Thr Gln Asn Ser Tyr 290 295 300 Gly Cys Ala Thr Ser Thr Pro Tyr Ser Thr Ser Arg Leu Met Leu Leu 305 310 315 320 Asn Met Pro Gly Gln Leu Pro Gln Thr Leu Ser Ser Pro Ser Thr Arg 325 330 335 Leu Ile Thr Glu Pro Pro Gln Ala Thr Leu Trp Ser Pro Ser Met Val 340 345 350 Cys Gly Met Thr Thr Pro Pro Thr Ser Pro Gly Asn Val Pro Pro Asp 355 360 365 Leu Ser His Pro Tyr Ser Lys Val Phe Gly Thr Thr Ala Gly Gly Lys 370 375 380 Gly Thr Pro Leu Gly Thr Pro Ala Thr Ser Pro Pro Pro Ala Pro Leu 385 390 395 400 Cys His Ser Asp Asp Tyr Val His Ile Ser Leu Pro Gln Ala Thr Val 405 410 415 Thr Pro Pro Arg Lys Glu Glu Arg Met Asp Ser Ala Arg Pro Cys Leu 420 425 430 His Arg Gln His His Leu Leu Asn Asp Arg Gly Ser Glu Glu Pro Pro 435 440 445 Gly Ser Lys Gly Ser Val Thr Leu Ser Asp Leu Pro Gly Phe Leu Gly 450 455 460 Asp Leu Ala Ser Glu Glu Asp Ser Ile Glu Lys Asp Lys Glu Glu Ala 465 470 475 480 Ala Ile Ser Arg Glu Leu Ser Glu Ile Thr Thr Ala Glu Ala Glu Pro 485 490 495 Val Val Pro Arg Gly Gly Phe Asp Ser Pro Phe Tyr Arg Asp Ser Leu 500 505 510 Pro Gly Ser Gln Arg Lys Thr His Ser Ala Ala Ser Ser Ser Gln Gly 515 520 525 Ala Ser Val Asn Pro Glu Pro Leu His Ser Ser Leu Asp Lys Leu Gly 530 535 540 Pro Asp Thr Pro Lys Gln Ala Phe Thr Pro Ile Asp Leu Pro Cys Gly 545 550 555 560 Ser Ala Asp Glu Ser Pro Ala Gly Asp Arg Glu Cys Gln Thr Ser Leu 565 570 575 Glu Thr Ser Ile Phe Thr Pro Ser Pro Cys Lys Ile Pro Pro Pro Thr 580 585 590 Arg Val Gly Phe Gly Ser Gly Gln Pro Pro Pro Tyr Asp His Leu Phe 595 600 605 Glu Val Ala Leu Pro Lys Thr Ala His His Phe Val Ile Arg Lys Thr 610 615 620 Glu Glu Leu Leu Lys Lys Ala Lys Gly Asn Thr Glu Glu Asp Gly Val 625 630 635 640 Pro Ser Thr Ser Pro Met Glu Val Leu Asp Arg Leu Ile Gln Gln Gly 645 650 655 Ala Asp Ala His Ser Lys Glu Leu Asn Lys Leu Pro Leu Pro Ser Lys 660 665 670 Ser Val Asp Trp Thr His Phe Gly Gly Ser Pro Pro Ser Asp Glu Ile 675 680 685 Arg Thr Leu Arg Asp Gln Leu Leu Leu Leu His Asn Gln Leu Leu Tyr 690 695 700 Glu Arg Phe Lys Arg Gln Gln His Ala Leu Arg Asn Arg Arg Leu Leu 705 710 715 720 Arg Lys Val Ile Lys Ala Ala Ala Leu Glu Glu His Asn Ala Ala Met 725 730 735 Lys Asp Gln Leu Lys Leu Gln Glu Lys Asp Ile Gln Met Trp Lys Val 740 745 750 Ser Leu Gln Lys Glu Gln Ala Arg Tyr Asn Gln Leu Gln Glu Gln Arg 755 760 765 Asp Thr Met Val Thr Lys Leu His Ser Gln Ile Arg Gln Leu Gln His 770 775 780 Asp Arg Glu Glu Phe Tyr Asn Gln Ser Gln Glu Leu Gln Thr Lys Leu 785 790 795 800 Glu Asp Cys Arg Asn Met Ile Ala Glu Leu Arg Ile Glu Leu Lys Lys 805 810 815 Ala Asn Asn Lys Val Cys His Thr Glu Leu Leu Leu Ser Gln Val Ser 820 825 830 Gln Lys Leu Ser Asn Ser Glu Ser Val Gln Gln Gln Met Glu Phe Leu 835 840 845 Asn Arg Gln Leu Leu Val Leu Gly Glu Val Asn Glu Leu Tyr Leu Glu 850 855 860 Gln Leu Gln Asn Lys His Ser Asp Thr Thr Lys Glu Val Glu Met Met 865 870 875 880 Lys Ala Ala Tyr Arg Lys Glu Leu Glu Lys Asn Arg Ser His Val Leu 885 890 895 Gln Gln Thr Gln Arg Leu Asp Thr Ser Gln Lys Arg Ile Leu Glu Leu 900 905 910 Glu Ser His Leu Ala Lys Lys Asp His Leu Leu Leu Glu Gln Lys Lys 915 920 925 Tyr Leu Glu Asp Val Lys Leu Gln Ala Arg Gly Gln Leu Gln Ala Ala 930 935 940 Glu Ser Arg Tyr Glu Ala Gln Lys Arg Ile Thr Gln Val Phe Glu Leu 945 950 955 960 Glu Ile Leu Asp Leu Tyr Gly Arg Leu Glu Lys Asp Gly Leu Leu Lys 965 970 975 Lys Leu Glu Glu Glu Lys Ala Glu Ala Ala Glu Ala Ala Glu Glu Arg 980 985 990 Leu Asp Cys Cys Asn Asp Gly Cys Ser Asp Ser Met Val Gly His Asn 995 1000 1005 Glu Glu Ala Ser Gly His Asn Gly Glu Thr Lys Thr Pro Arg Pro Ser 1010 1015 1020 Ser Ala Arg Gly Ser Ser Gly Ser Arg Gly Gly Gly Gly Ser Ser Ser 1025 1030 1035 1040 Ser Ser Ser Glu Leu Ser Thr Pro Glu Lys Pro Pro His Gln Arg Ala 1045 1050 1055 Gly Pro Phe Ser Ser Arg Trp Glu Thr Thr Met Gly Glu Ala Ser Ala 1060 1065 1070 Ser Ile Pro Thr Thr Val Gly Ser Leu Pro Ser Ser Lys Ser Phe Leu 1075 1080 1085 Gly Met Lys Ala Arg Glu Leu Phe Arg Asn Lys Ser Glu Ser Gln Cys 1090 1095 1100 Asp Glu Asp Gly Met Thr Ser Ser Leu Ser Glu Ser Leu Lys Thr Glu 1105 1110 1115 1120 Leu Gly Lys Asp Leu Gly Val Glu Ala Lys Ile Pro Leu Asn Leu Asp 1125 1130 1135 Gly Pro His Pro Ser Pro Pro Thr Pro Asp Ser Val Gly Gln Leu His 1140 1145 1150 Ile Met Asp Tyr Asn Glu Thr His His Glu His Ser 1155 1160 23 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 3 CCAGAGACAA AGTTGCAAAA CAG 23 25 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 4 TTGATTACAG TTTGCATTTC TTGAC 25 20 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 5 AAAGCAGAGG AGAGAGCAGG 20 22 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 6 CCTAAAACCA CACACTAACC CC 22 19 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 7 AAGGCAGGCC AAAACCAAC 19 22 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 8 TGACTTAGCA TTCCTTTGCC AC 22 19 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 9 AGTGAGTCAC TGTGCCTGG 19 21 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 10 TGTTCTGCCC TTGTCTCTAA G 21 19 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 11 CCAATTAGAA GAGGCAAGC 19 20 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 12 GCAACATTTT TCGTCTTGTG 20 21 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 13 GAGAGTGCCC CAGTCCCTTA C 21 20 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 14 CCAGGTGGAA TACCGACTGC 20 24 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 15 TGGATTTGGA GCTAAAGTAA CAAC 24 22 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 16 CGTTTTTTTC TTGGTAAGAT CG 22 22 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 17 TCATGCTGAC CCAAAACAAA AC 22 19 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 18 AAAGGCATTT CTGCCACCC 19 19 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 19 ACTGACTGCC TCCCTCCCC 19 22 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 20 TCGCAGTGTG TGTTAAATTG CC 22 24 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 21 ACCTGTCTGA AGGAAGAATG TTAG 24 20 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 22 CCTCAAACTT CATGTCCACG 20 20 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 23 ACTGTCTGGG TCTGAAACGC 20 22 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 24 TTTATGTCGT CGGATTTTTC AC 22 22 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 25 CACAGTCCTT ATGCTGGAAT TG 22 25 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 26 TTTTTTTCAG GAAGTAGAAA TGATG 25 19 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 27 CCTCCTGTTC TGTGCCAAC 19 21 base pairs nucleic acid single linear other nucleic acid /desc = “PCR primer” NO NO 28 TCACCAGCTC CTTTTTTCCT C 21 

What is claimed is:
 1. A method of identifying a patient that has or is likely to develop tuberous sclerosis, said method comprising: a) determining if the TSC-1 gene of said patient contains a mutation when compared to SEQ ID NO:1, wherein said mutation occurs at a site selected from: I) in exon 7: position 865; ii) in exon 9: position 966; 970; 993; or 1112; iii) in exon 10: position 1207; iv) in exon 15: position 1746; 1750; 1801; 1892; 1929; 1942; 2009; 2041; 2060; 2105; 2122; 2126; or 2176; v) in exon 17: position 2295; 2324; 2332; or 2395; vi) in exon 18: position 2448; 2519; 2540; 2577; or 2583; vii) in exon 19: position 2691; viii) in exon 20: position 2724; or 2730; and b) concluding that said patient is at increased risk of having or developing tuberous sclerosis if said mutation is present.
 2. The method of claim 1, wherein said mutation is selected from the group consisting of: a) in exon 7: 865delTT; b) in exon 9: 966delA; 970TG; 993G▾T; or 1112T▾G; c) in exon 10: 1207delCT; d) in exon 15: 1746C▾T; 1750delCA; 1801delAG; 1892del23; 1929delAG; 1942delGGinsTTGA; 2009delT; 2041delTT; 2060delA; 2105delAAAG; 2122delAC; 2126delAG; or 2176delTG; e) in exon 17: 2295C▾T; 2324duplGTTACTC; 2332delAT; or 2395insA; f) in exon 18: 2448C▾T; 2519del23bp; 2540delC; 2577C▾T; and 2583G▾T; g) in exon 19: 2691delAC; h) in exon 20: 2724-1G▾T; or 2730insA.
 3. A method of identifying a patient that has or is likely to develop tuberous sclerosis, said method comprising: a) determining if the TSC-1 gene of said patient is mutated such that, relative to SEQ ID NO:2, one or more of the following amino acid changes occur in the encoded gene product: L250X; E258X; Y297X; R509X; R692X; Q743X; R786X; or E788X; and b) concluding that said patient is at increased risk of having or developing tuberous sclerosis if one or more of said following amino acid changes are found to occur.
 4. The method of any one of claims 1-3, wherein said method comprises amplifying one or more regions of the TSC-1 gene by polymerase chain reaction and analyzing amplification products produced by said polymerase chain reaction for mutations.
 5. The method of claim 4, wherein said analyzing of amplification products is accomplished by performing heteroduplex or single stand conformation polymorphism analysis. 